The suspected serial killer of three Brooklyn shopkeepers has been charged after investigators matched ballistic evidence from each of the shootings to a gun recovered at his girlfriend’s home, a law enforcement official said.

Police picked him up in Bay Ridge Tuesday afternoon while investigating the most recent slaying in a series of deadly shootings of Brooklyn business owners of Middle Eastern descent dating back to July.

Authorities had said they were looking to question a person they called “John Doe Duffel Bag,” the balding man with a mustache who was seen on surveillance video near the scene of the latest slaying and who was linked to a video in an earlier incident.

Law enforcement sources say Perrone made statements placing himself near the scene of the shooting at the Valentino Fashion Inc. in Bay Ridge on July 6. Mohamed Gebeli, 65, an Egyptian immigrant and a Muslim, was found shot in the back of his shop. Detectives found .22-caliber gun shell casings at that crime scene and also at the scene where Isaac Kadare, 59, also Egyptian but Jewish, was shot in the head in his Amazing 99 Cent Deal store Aug. 6.

The latest victim, 78-year-old Rahmatollah Vahidipour, a Jewish man from Iran, was killed in his women’s clothing boutique on Flatbush Avenue Friday. The same casings were found at that scene.

A law enforcement official said a Ruger rifle with a sawed-off stock and an improvised combination laser/light attached to its barrel was found early Wednesday in a duffel bag at the suspect’s girlfriend’s Brooklyn home. Also contained in the bag were 30 copper-coated hollow-point bullets, latex gloves, women’s clothing, a 12-inch steak knife with a substance that may be blood, a fabric color chart and black plastic bags with a substance that may be blood on it, the source said.

Authorities say it is the same duffel bag seen in the surveillance video at the scene of two slayings. The weapon uses .22 ammunition consistent with ballistics found at each of the three crime scenes connected to the case, law enforcement sources said.

Authorities also found .22 caliber ammunition, three knives, one of which appeared to have blood on it, black gloves and women’s pantyhose with the legs cut off in the duffel bag, a law enforcement official said. The blood on the recovered knife is being tested for DNA evidence.

Law enforcement sources say the man’s girlfriend and ex-wife are cooperating with detectives. Sources say he is a fabric and garment salesman, and has several prior arrests, including for stalking and burglary, in Pennsylvania.

A woman who lived across the street from the suspect’s former home on Staten Island said the divorced father of one was a peculiar neighbor and that he used to sing opera loudly from his front yard at odd hours of the night.

“He was just that crazy neighbor,” said Julia Marra, 21, who viewed the suspect as harmless.

It appeared the suspect was trying to sell his home on the corner of Clove Road and Beverly Avenue on Staten Island. The structure is visibly in disrepair and in need of rehabilitation. A phone number listed on the for sale sign in the yard connected to the voice mailbox of the suspect.

Detectives who specialize in hate crimes and FBI analysts who specialize in behavioral analysis joined the case this week, authorities said.

“The possibility of a bias motive here is something that can’t be excluded,” Police Commissioner Ray Kelly said Monday.

The bodies were all partially obscured by clothing or, in one case, a box. The shops all lacked surveillance cameras, and the owners were alone in the store. The locations of the shops are each about 4 miles apart, with addresses that contain the number eight. Money was taken from everyone but Vahidipour, who had $171 in his pocket.

Kelly said it’s reasonable to think the shooter had canvassed the area to find locations where no cameras existed.

“Here you have three stores where the proprietor is there by himself, no cameras in any of these,” he said. “You’d have to speculate that some sort of reconnaissance was going on before the murders took place.”